Relevant bibliographies by topics / DNA Fragment Assembly

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'DNA Fragment Assembly'

Author: Grafiati
Published: 4 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "DNA Fragment Assembly"

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Colloms, Sean D., Christine A. Merrick, Femi J. Olorunniji, et al. "Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination." Nucleic Acids Research 42, no. 4 (2013): e23-e23. http://dx.doi.org/10.1093/nar/gkt1101.

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Abstract Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial
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Rathee, Manisha, and T. V. Vijay Kumar. "DNA Fragment Assembly Using Multi-Objective Genetic Algorithms." International Journal of Applied Evolutionary Computation 5, no. 3 (2014): 84–108. http://dx.doi.org/10.4018/ijaec.2014070105.

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DNA Fragment Assembly Problem (FAP) is concerned with the reconstruction of the target DNA, using the several hundreds (or thousands) of sequenced fragments, by identifying the right order and orientation of each fragment in the layout. Several algorithms have been proposed for solving FAP. Most of these have solely dwelt on the single objective of maximizing the sum of the overlaps between adjacent fragments in order to optimize the fragment layout. This paper aims to formulate this FAP as a bi-objective optimization problem, with the two objectives being the maximization of the overlap betwe
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Adithya B. and Santhi G. "DNA Cryptography Using DNA Fragment Assembly and Fragment Key Expansion for Genomic Data." International Journal of Organizational and Collective Intelligence 12, no. 2 (2022): 1–19. http://dx.doi.org/10.4018/ijoci.286173.

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This research proposes a tweaked scheme based on DNA fragment assembly to improve protection over insecure channel. The proposed procedure utilizes binary coding to change over an underlying plaintext into a reference DNA arrangement to deal with the fragmentation. DNA fragment key expansion is applied over the reference DNA sequence to make the short-chain fragments. The redundancy in the long-chain of reference DNA is removed using DNA fragment assembly. A look-up table is generated to store the binary values of overlapped fragments to be reassembled during the encryption and decryption proc
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Gheraibia, Youcef, Abdelouahab Moussaoui, Sohag Kabir, and Smaine Mazouzi. "Pe-DFA." International Journal of Applied Metaheuristic Computing 7, no. 2 (2016): 58–70. http://dx.doi.org/10.4018/ijamc.2016040104.

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DNA Fragment Assembly (DFA) is a process of finding the best order and orientation of a set of DNA fragments to reconstruct the original DNA sequence from them. As it has to consider all possible combinations among the DNA fragments, it is considered as a combinatorial optimisation problem. This paper presents a method showing the use of Penguins Search Optimisation Algorithm (PeSOA) for DNA fragment assembly problem. Penguins search optimisation is a nature inspired metaheuristic algorithm based on the collaborative hunting strategy of penguins. The approach starts its operation by generating
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ANGELERI, E., B. APOLLONI, D. DE FALCO, and L. GRANDI. "DNA FRAGMENT ASSEMBLY USING NEURAL PREDICTION TECHNIQUES." International Journal of Neural Systems 09, no. 06 (1999): 523–44. http://dx.doi.org/10.1142/s0129065799000563.

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The paper describes an alternative approach to the fragment assembly problem. The key idea is to train a recurrent neural network to tracking the sequence of bases constituting a given fragment and to assign to a same cluster all the sequences which are well tracked by this network. We make use of a 3-layer Recurrent Perceptron and examine both edited sequences from a ftp site and artificial fragments from a common simulation software: the clusters we obtain exhibit interesting properties in terms of error filtering, stability and self consistency; we define as well, with a certain degree of a
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Semashko, T. A., G. Y. Fisunov, E. A. Tsoy, et al. "Modern Approaches to de novo Synthesis of Extended DNA Fragments: Assembly of a Wide Repertoire of Sequences." Acta Naturae 16, no. 1 (2024): 77–85. http://dx.doi.org/10.32607/actanaturae.27362.

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The standardization of DNA fragment assembly methods for many tasks of synthetic biology is crucial. This is necessary for synthesizing a wider repertoire of sequences, as well as for further automation and miniaturization of such reactions. In this work, we proposed conditions for the assembly of DNA fragments from chemically synthesized oligonucleotides and we identified the errors occurring in the sequence under these conditions. Additionally, we proposed conditions for further combining synthetic fragments into larger DNA fragments. We showed that the optimized conditions are suitable for
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Yang, Kun, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, and Joel S. Bader. "BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts." Bioinformatics 32, no. 6 (2015): 937–39. http://dx.doi.org/10.1093/bioinformatics/btv664.

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Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with a
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Beeram, Satyanarayana Reddy, and Edara Srinivasa Reddy. "A Study of DNA Fragment Assembly Algorithms." Journal of Applied Physics and Engineering 1, no. 1 (2016): 10–16. http://dx.doi.org/10.26524/jap2.

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Raja, G., and U. Srinivasulu Reddy. "DNA Fragment Assembly Using Hybridized Catfish PSO." International Journal of Software Innovation 9, no. 2 (2021): 69–80. http://dx.doi.org/10.4018/ijsi.2021040104.

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DNA fragment assembly aids in uncovering several aspects of the human DNA, and hence in-turn enables scientists in understanding and curing several hereditary problems. Several computational methods have been proposed to solve this problem. However, the huge size and the NP-hard nature of the problem poses several challenges in proposing a time effective system for fragment assembly. This paper proposes a hybridized catfish PSO model for the process of fragment assembly. PSO algorithm is enhanced by incorporating the catfish particles to enable the model to get out of the local optimal solutio
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Quiroz-Ibarra, J., Guillermo Mallén-Fullerton, and Guillermo Fernández-Anaya. "DNA Paired Fragment Assembly Using Graph Theory." Algorithms 10, no. 2 (2017): 36. http://dx.doi.org/10.3390/a10020036.

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Dissertations / Theses on the topic "DNA Fragment Assembly"

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Adi, Said Sadique. "Ferramentas de auxílio ao seqüenciamento de DNA por montagem de fragmentos: um estudo comparativo." Universidade de São Paulo, 2000. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-26112001-150157/.

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Atualmente, existe um grande número de ferramentas para montagem de fragmentos de DNA disponíveis. Neste trabalho apresentamos um estudo comparativo das ferramentas CAP2, FAKtory, TIGR e PHRAP. Para realizarmos este estudo, primeiramente executamos esses sistemas de montagem sobre 12 casos de testes distintos. Após isso, tomamos os resultados obtidos por cada um deles e os comparamos com as seqüências de onde os fragmentos foram originalmente obtidos. Os testes utilizados avaliam a eficiências dos programas com relação a três problemas associados ao processo de montagem (erros no sequenciament
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Book chapters on the topic "DNA Fragment Assembly"

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Alba, Enrique, and Bernabè Dorronsoro. "Bioinformatics: The DNA Fragment Assembly Problem." In Operations Research/Computer Science Interfaces Series. Springer US, 2008. http://dx.doi.org/10.1007/978-0-387-77610-1_15.

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Milanesi, L., M. Marsilli, G. Mauri, C. Rolfi, and L. Uboldi. "Fragment assembly system for DNA sequencing projects." In DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999. http://dx.doi.org/10.1090/dimacs/047/12.

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Meidanis, João. "A simple toolkit for DNA fragment assembly." In DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999. http://dx.doi.org/10.1090/dimacs/047/14.

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Wetcharaporn, Wannasak, Nachol Chaiyaratana, and Sissades Tongsima. "DNA Fragment Assembly: An Ant Colony System Approach." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11732242_21.

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Yassine, Asmae, Morad Bouzidi, and Mohammed Essaid Riffi. "Cat Swarm Optimization Algorithm for DNA Fragment Assembly Problem." In International Conference on Advanced Intelligent Systems for Sustainable Development. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-26384-2_57.

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Abdel-Basset, Mohamed, Ripon K. Chakrabortty, and Reda Mohamed. "Role of Advanced Metaheuristics for DNA Fragment Assembly Problem." In Application of Advanced Optimization Techniques for Healthcare Analytics. CRC Press, 2023. http://dx.doi.org/10.1201/9781003325574-5.

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Wetcharaporn, Wannasak, Nachol Chaiyaratana, and Sissades Tongsima. "DNA Fragment Assembly by Ant Colony and Nearest Neighbour Heuristics." In Artificial Intelligence and Soft Computing – ICAISC 2006. Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11785231_106.

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Alba, Enrique, and Gabriel Luque. "A Hybrid Genetic Algorithm for the DNA Fragment Assembly Problem." In Recent Advances in Evolutionary Computation for Combinatorial Optimization. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-70807-0_7.

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Si, Shuqing, Ben Cao, Qi Shao, et al. "Efficient DNA Fragment Assembly Based on Discrete Slime Mould Algorithm." In Lecture Notes in Computer Science. Springer Nature Singapore, 2025. https://doi.org/10.1007/978-981-96-8298-0_20.

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Alba, Enrique, and Gabriel Luque. "A New Local Search Algorithm for the DNA Fragment Assembly Problem." In Evolutionary Computation in Combinatorial Optimization. Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-71615-0_1.

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Conference papers on the topic "DNA Fragment Assembly"

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Mallen-Fullerton, Guillermo M., and Guillermo Fernandez-Anaya. "DNA fragment assembly using optimization." In 2013 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2013. http://dx.doi.org/10.1109/cec.2013.6557749.

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Quan, Guang-Ri, Yong-Dong Xu, Ya-Dong Wang, and Zhi-Ming Xu. "A New DNA Fragment Assembly Method Based on Long Fragment Filtration." In 2008 International Conference on Biomedical Engineering And Informatics (BMEI). IEEE, 2008. http://dx.doi.org/10.1109/bmei.2008.175.

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Pevzner, Pavel A., Haixu Tang, and Michael S. Waterman. "A new approach to fragment assembly in DNA sequencing." In the fifth annual international conference. ACM Press, 2001. http://dx.doi.org/10.1145/369133.369230.

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Hughes, James, Sheridan Houghten, Guillermo M. Mallen-Fullerton, and Daniel Ashlock. "Recentering and Restarting Genetic Algorithm variations for DNA Fragment Assembly." In 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2014. http://dx.doi.org/10.1109/cibcb.2014.6845500.

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Hassan, Hasniliati, Zulkifli Abd Majid, Abdul Karimi Halim, and Azlina Ibrahim. "Design and development of DNA fragment assembly using IWP method." In 2013 IEEE 4th Control and System Graduate Research Colloquium (ICSGRC). IEEE, 2013. http://dx.doi.org/10.1109/icsgrc.2013.6653277.

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Ulker, Ezgi Deniz. "Adaptation of harmony search algorithm for DNA fragment assembly problem." In 2016 SAI Computing Conference (SAI). IEEE, 2016. http://dx.doi.org/10.1109/sai.2016.7555973.

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Cai, Kui, and Jincai Yang. "PMMR: A Method for Masking Repeats in DNA Fragment Assembly." In 2009 Asia-Pacific Conference on Information Processing, APCIP. IEEE, 2009. http://dx.doi.org/10.1109/apcip.2009.139.

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Huang, Ko-Wei, Jui-Le Chen, and Chu-Sing Yang. "A Hybrid PSO-Based Algorithm for Solving DNA Fragment Assembly Problem." In 2012 3rd International Conference on Innovations in Bio-Inspired Computing and Applications (IBICA). IEEE, 2012. http://dx.doi.org/10.1109/ibica.2012.8.

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Firoz, Jesun Sahariar, M. Sohel Rahman, and Tanay Kumar Saha. "Hybrid meta-heuristics for DNA fragment assembly problem for noiseless data." In 2012 International Conference on Informatics, Electronics & Vision (ICIEV). IEEE, 2012. http://dx.doi.org/10.1109/iciev.2012.6317502.

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Dorronsoro, Bernabe, Enrique Alba, Gabriel Luque, and Pascal Bouvry. "A self-adaptive cellular memetic algorithm for the DNA fragment assembly problem." In 2008 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2008. http://dx.doi.org/10.1109/cec.2008.4631154.

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Reports on the topic "DNA Fragment Assembly"

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Ohad, Itzhak, and Himadri Pakrasi. Role of Cytochrome B559 in Photoinhibition. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7613031.bard.

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The aim of this research project was to obtain information on the role of the cytochrome b559 in the function of Photosystem-II (PSII) with special emphasis on the light induced photo inactivation of PSII and turnover of the photochemical reaction center II protein subunit RCII-D1. The major goals of this project were: 1) Isolation and sequencing of the Chlamydomonas chloroplast psbE and psbF genes encoding the cytochrome b559 a and b subunits respectively; 2) Generation of site directed mutants and testing the effect of such mutation on the function of PSII under various light conditions; 3)
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